= Little Rock, Arkansas, USA: January 24-26, 2024 = <)>> Three-day Brainstorm training, MEG- and EEG-oriented.<
>During the first two days, participants will process an EEG/MEG dataset to learn and explore Brainstorm features. On the last day, participants are encouraged to bring their own data, which we will review in small groups. == General information == <)>> <)>>'''Where'''<)>> [[https://www.archildrens.org|Arkansas Children's Hospital]]<)>> <)>>'''When'''<)>>January 24-26, 2024, 9:00-16:30<)>> <)>>'''Registration'''<)>> '''Closed''' <)>> <)>>'''Organizers'''<)>>[[https://www.archildrens.org/research/researchers/diana-escalona-vargas|Diana Escalona-Vargas]]<
> (Arkansas Children's Hospital, USA)<)>> <)>>'''Instructors'''<)>>[[AboutUs/SylvainBaillet|Sylvain Baillet]] and [[AboutUs/RaymundoCassani|Raymundo Cassani]] <
> (Montreal Neurological Institute / McGill, Canada)<)>> <)>>'''Audience'''<)>>Users interested in analyzing MEG/EEG recordings using Brainstorm.<
>Some experience with MEG/EEG is recommended. Teaching in English.<
>Participants are required to have an academic affiliation <)>> <)>>'''Slides'''<)>> [[https://box.bic.mni.mcgill.ca/s/H9QmxHuNlr1c1Ld|Intro slides]] | [[https://box.bic.mni.mcgill.ca/s/X1CaQHE9JV6BWN9|Lectures slides]] | [[https://box.bic.mni.mcgill.ca/s/vgMLfe30Ky5ZLxn|Walkthrough]] | [[https://forms.gle/b8LtFjp1pN1TZvf4A|Survey]] <)>> <)>> == Requirements == In order to make the workshop as efficient as possible, we ask all the attendees to: <)>>'''download, install and test'''<)>> the software and <)>>'''download'''<)>> the workshop dataset on their laptops prior to the workshop. == Installing Brainstorm == Please read carefully the following instructions on: <
>[[WorkshopGeneralInstall|preparing your laptop for the training]] == Workshop dataset == The workshop dataset is based on the Frontiers Research Topic [[https://www.frontiersin.org/research-topics/5158/from-raw-megeeg-to-publication-how-to-perform-megeeg-group-analysis-with-free-academic-software|From raw MEG/EEG to publication]]: a collection of articles reporting the analysis of the [[https://openneuro.org/datasets/ds000117|same multimodal dataset]] using different software environments. During this workshop, first we will go through the main processing steps using data from one of the participants following the processing pipeline described in the article [[https://www.frontiersin.org/articles/10.3389/fnins.2019.00076/full|MEG/EEG Group Analysis With Brainstorm]] and the corresponding [[https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle|online tutorial]]. In a second part, we will use pre-processed data from two participants to show the steps for group analysis. Once you have successfully installed and tested Brainstorm (see previous section), proceed to download the dataset for the workshop. 1. Download the tutorial dataset: '''`ds000117_S1R1.zip`''' (820 MB):<
> https://box.bic.mni.mcgill.ca/s/AFXWFz4mC7C2l6V 1. Unzip the downloaded file on your desktop: it will create a new folder named `ds000117_S1R1`. It contains raw data for one participant, one run. 1. Download the tutorial dataset: '''`Arkansas_S1S2_R1R2.zip`''' (920 MB):<
> https://box.bic.mni.mcgill.ca/s/goTIK9p0PI98ZBD 1. Unzip the downloaded file on your desktop: it will create a new folder named `Arkansas_S1S2_R1R2`. It contains pre-processed data for two participants, two runs ech. 1. Final check: after following the steps above, you should have 4 folders on your desktop: * '''`brainstorm3`''': the software folder, containing the source code and the compiled executable * '''`brainstorm_db`''': your Brainstorm database (which should be empty for now) * '''`ds000117_S1R1`''': Dataset 1 used during the workshop session * '''`Arkansas_S1S2_R1R2`''': Dataset 2 used during the workshop session == Program == === Day 1 === <)>> <)>>08:30-09:00<)>> Onsite assistance in installing the material for the training session<)>> <)>>09:00-09:30<)>>'''Biological origins of MEG and EEG''' ''(lecture S. Baillet)''<)>> <)>>09:30-10:00<)>>'''Introduction to Brainstorm''' ''(lecture R. Cassani)''<)>> <)>>10:30-11:20<)>>'''Loading anatomy and recordings''' Brainstorm database Set anatomy Review RAW recordings Events and event functions <)>> <)>>11:20-12:00<)>>'''Pre-processing''' Frequency filters Artifact detection Artifact correction with SSP <)>> <)>>12:00-13:00<)>>''Lunch''<)>> <)>>13:00-13:45<)>>'''Pre-processing (cont.)''' Artifact correction with SSP <)>> <)>>13:45-14:30<)>>'''Epoching and Importing''' Import epochs and sensor averages Visualization of epochs/trials Average trials <)>> <)>>14:30-15:00<)>> '''Spectral and time-frequency analysis of MEG/EEG signals''' ''(lecture S. Baillet)''<)>> <)>>15:00-15:45<)>>'''Time-frequency analysis''' Time-frequency representation of EEG/MEG signals <)>> <)>>15:45-16:00<)>>'''Day 1 wrap-up''' <)>> <)>> === Day 2 === <)>> <)>>08:30-09:00<)>> Onsite assistance, materials, concepts, day 1 steps<)>> <)>>09:00-09:45<)>>'''Source modelling''' ''(Lecture S. Baillet)''<)>> <)>>09:45-11:30<)>>'''Sources estimation ''' Forward model (aka Head model) Noise covariance matrix Source estimation <)>> <)>>11:30-12:00<)>>'''Sources estimation ''' Cortex parcellations: Atlases and Scouts <)>> <)>>12:00-13:00<)>>'''ACRI Visiting Scholars Research Seminar''' ''(Lecture S. Baillet)'' <
> Lunch will be provided <)>> <)>>13:00-13:30<)>>'''Subject level statistics''' Statistics, sensor space Statistics, source space <)>> <)>>13:30-14:00<)>>'''Sharing Protocols''' Exporting protocols Importing protocols Load provided protocol: 2 participants, 2 runs each <)>> <)>>14:00-15:30<)>>'''Subject level analysis''' Subject averages (sensors, sources, and time-frequency) Within subject differences <)>> <)>>15:30-16:30<)>>'''Group level analysis''' Preparing source subject-averages Co-registration to default anatomy Group averages <)>> <)>> === Day 3 === <)>> <)>>09:00-09:30<)>>'''Connectivity & resting-state & evoked response''' ''(Lecture S. Baillet)''<)>> <)>>09:30-10:00<)>>'''Connectivity''' Functional connectivity <)>> <)>>10:00-11:00<)>>'''Beyond the GUI''' Scripting GitHub <)>> <)>>11:00-12:00<)>>'''Participants working with their own data'''<)>> <)>>12:00-13:00<)>>''Lunch''<)>> <)>>12:00-15:30<)>>'''Participants working with their own data (cont.)'''<)>> <)>>16:15-16:30<)>>'''Wrap-up''' <)>> == Bring your own data == The last session will be mostly dedicated to addressing participants' requests. We encourage you to bring in your own sample of MEG/EEG data that you would be interested in processing with Brainstorm. We may ask that you pair with other attendees, for logistics purposes. The file formats that can be read by Brainstorm are listed on the [[http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats|Introduction page]]. Please contact us in advance if you are not sure your dataset can be imported in Brainstorm. If you do not have data available, you may continue to use the tutorial dataset used in the present workshop. We provide [[https://box.bic.mni.mcgill.ca/s/vgMLfe30Ky5ZLxn|a detailed step-by-step walkthrough]] of the data analyses performed at the training. == Troubleshooting == For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )